Theoretical Studies of Molecular Interactions, Dynamics, Structure, and Free Energies of Biological Systems PDF Download

Author: Dat Huy Nguyen
Publisher:
ISBN:
Category :
Languages : en
Pages : 364

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Author: Kevin Naidoo
Publisher: Royal Society of Chemistry
ISBN: 1847555373
Category : Science
Languages : en
Pages : 305

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Book Description
Computational and theoretical tools for understanding biological processes at the molecular level is an exciting and innovative area of science. Using these methods to study the structure, dynamics and reactivity of biomacromolecules in solution, computational chemistry is becoming an essential tool, complementing the more traditional methods for structure and reactivity determination. Modelling Molecular Structure and Reactivity in Biological Systems covers three main areas in computational chemistry; structure (conformational and electronic), reactivity and design. Initial sections focus on the link between computational and spectroscopic methods in the investigation of electronic structure. The use of Free Energy calculations for the elucidation of reaction mechanisms in enzymatic systems is also discussed. Subsequent sections focus on drug design and the use of database methods to determine ADME (absorption, distribution, metabolism, excretion) properties. This book provides a complete reference on state of the art computational chemistry practised on biological systems. It is ideal for researchers in the field of computational chemistry interested in its application to biological systems.

Author: Leif A. Eriksson
Publisher: Elsevier
ISBN: 0080542700
Category : Science
Languages : en
Pages : 719

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Book Description
Theoretical chemistry has been an area of tremendous expansion and development over the past decade; from an approach where we were able to treat only a few atoms quantum mechanically or make fairly crude molecular dynamics simulations, into a discipline with an accuracy and predictive power that has rendered it an essential complementary tool to experiment in basically all areas of science. This volume gives a flavour of the types of problems in biochemistry that theoretical calculations can solve at present, and illustrates the tremendous predictive power these approaches possess.A wide range of computational approaches, from classical MD and Monte Carlo methods, via semi-empirical and DFT approaches on isolated model systems, to Car-Parinello QM-MD and novel hybrid QM/MM studies are covered. The systems investigated also cover a broad range; from membrane-bound proteins to various types of enzymatic reactions as well as inhibitor studies, cofactor properties, solvent effects, transcription and radiation damage to DNA.

Author: David A. Micha
Publisher: John Wiley & Sons
ISBN: 0470290749
Category : Science
Languages : en
Pages : 400

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Book Description
A modern, comprehensive text and reference describing intermolecular forces, this book begins with coverage of the concepts and methods for simpler systems, then moves on to more advanced subjects for complex systems – emphasizing concepts and methods used in calculations with realistic models and compared with empirical data. Contains applications to many physical systems and worked examples Proceeds from introductory material to advanced modern treatments Has relevance for new materials, biological phenomena, and energy and fuels production

Author: Hagai Meirovitch
Publisher: CRC Press
ISBN: 1000072304
Category : Computers
Languages : en
Pages : 374

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Book Description
Computer simulation has become the main engine of development in statistical mechanics. In structural biology, computer simulation constitutes the main theoretical tool for structure determination of proteins and for calculation of the free energy of binding, which are important in drug design. Entropy and Free Energy in Structural Biology leads the reader to the simulation technology in a systematic way. The book, which is structured as a course, consists of four parts: Part I is a short course on probability theory emphasizing (1) the distinction between the notions of experimental probability, probability space, and the experimental probability on a computer, and (2) elaborating on the mathematical structure of product spaces. These concepts are essential for solving probability problems and devising simulation methods, in particular for calculating the entropy. Part II starts with a short review of classical thermodynamics from which a non-traditional derivation of statistical mechanics is devised. Theoretical aspects of statistical mechanics are reviewed extensively. Part III covers several topics in non-equilibrium thermodynamics and statistical mechanics close to equilibrium, such as Onsager relations, the two Fick's laws, and the Langevin and master equations. The Monte Carlo and molecular dynamics procedures are discussed as well. Part IV presents advanced simulation methods for polymers and protein systems, including techniques for conformational search and for calculating the potential of mean force and the chemical potential. Thermodynamic integration, methods for calculating the absolute entropy, and methodologies for calculating the absolute free energy of binding are evaluated. Enhanced by a number of solved problems and examples, this volume will be a valuable resource to advanced undergraduate and graduate students in chemistry, chemical engineering, biochemistry biophysics, pharmacology, and computational biology.

Author: G. Vergoten
Publisher: Springer Science & Business Media
ISBN: 9401154848
Category : Science
Languages : en
Pages : 327

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Book Description
Biomolecular Structure and Dynamics describes recent fundamental advances in the experimental and theoretical study of molecular dynamics and stochastic dynamic simulations, X-ray crystallography and NMR of biomolecules, the structure of proteins and its prediction, time resolved Fourier transform IR spectroscopy of biomolecules, the computation of free energy, applications of vibrational CD of nucleic acids, and solid state NMR. Further presentations include recent advances in UV resonance Raman spectroscopy of biomolecules, semiempirical MO methods, empirical force fields, quantitative studies of the structure of proteins in water by Fourier transform IR, and density functional theory. Metal-ligand interactions, DFT treatment of organometallic and biological systems, and simulation vs. X-ray and far IR experiments are also discussed in some detail. The book provides a broad perspective of the current theoretical aspects and recent experimental findings in the field of biomolecular dynamics, revealing future research trends, especially in areas where theoreticians and experimentalists could fruitfully collaborate.

Author: W.F. van Gunsteren
Publisher: Springer Science & Business Media
ISBN: 9401711208
Category : Technology & Engineering
Languages : en
Pages : 633

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Book Description
The third volume in the series on Computer Simulation of Biomolecular Systems continues with the format introduced in the first volume [1] and elaborated in the second volume [2]. The primary emphasis is on the methodological aspects of simulations, although there are some chapters that present the results obtained for specific systems of biological interest. The focus of this volume has changed somewhat since there are several chapters devoted to structure-based ligand design, which had only a single chapter in the second volume. It seems useful to set the stage for this volume by quoting from my preface to Volume 2 [2]. "The long-range 'goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involv ing the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest." ...

Author: Jannis Samios
Publisher: Springer Science & Business Media
ISBN: 1402023847
Category : Science
Languages : en
Pages : 548

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Book Description
The unique behavior of the "liquid state", together with the richness of phenomena that are observed, render liquids particularly interesting for the scientific community. Note that the most important reactions in chemical and biological systems take place in solutions and liquid-like environments. Additionally, liquids are utilized for numerous industrial applications. It is for these reasons that the understanding of their properties at the molecular level is of foremost interest in many fields of science and engineering. What can be said with certainty is that both the experimental and theoretical studies of the liquid state have a long and rich history, so that one might suppose this to be essentially a solved problem. It should be emphasized, however, that although, for more than a century, the overall scientific effort has led to a considerable progress, our understanding of the properties of the liquid systems is still incomplete and there is still more to be explored. Basic reason for this is the "many body" character of the particle interactions in liquids and the lack of long-range order, which introduce in liquid state theory and existing simulation techniques a number of conceptual and technical problems that require specific approaches. Also, many of the elementary processes that take place in liquids, including molecular translational, rotational and vibrational motions (Trans. -Rot. -Vib. coupling), structural relaxation, energy dissipation and especially chemical changes in reactive systems occur at different and/or extremely short timescales.

Author:
Publisher: Academic Press
ISBN: 0128211350
Category : Science
Languages : en
Pages : 552

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Book Description
Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field

Author: Jiong Zhang
Publisher:
ISBN:
Category :
Languages : en
Pages : 152

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Book Description
The research presented in this thesis is relevant for the study of structure, function and dynamics of complex bio-molecular systems. The thesis contains two parts related to (1) protein structure prediction, and (2) free energy profile calculations in nano-scale systems. The new contributions reported in this thesis include (1) the development of the Selective Refinement (SR) protocol and the extension of the Molecular Dynamics Ranking (MDR) selection method for protein structure prediction, and (2) the formulation of the generalized FR (GFR) method for calculating the potential of mean force and the determination of the effective dynamics along one dimensional reaction coordinates in bio-molecular systems.